/* This file is part of the Gudhi Library. The Gudhi library
* (Geometric Understanding in Higher Dimensions) is a generic C++
* library for computational topology.
*
* Author(s): Vincent Rouvreau
* Pawel Dlotko - 2017 - Swansea University, UK
*
* Copyright (C) 2014 Inria
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see .
*/
#include
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#include "alpha_complex_3d_helper.h"
// Traits
using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
using PK = CGAL::Periodic_3_regular_triangulation_traits_3;
// Vertex type
using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>;
using Vb = CGAL::Regular_triangulation_vertex_base_3;
using AsVb = CGAL::Alpha_shape_vertex_base_3;
// Cell type
using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>;
using Cb = CGAL::Regular_triangulation_cell_base_3;
using AsCb = CGAL::Alpha_shape_cell_base_3;
using Tds = CGAL::Triangulation_data_structure_3;
using P3RT3 = CGAL::Periodic_3_regular_triangulation_3;
using Alpha_shape_3 = CGAL::Alpha_shape_3;
using Point_3 = P3RT3::Bare_point;
using Weighted_point_3 = P3RT3::Weighted_point;
// filtration with alpha values needed type definition
using Alpha_value_type = Alpha_shape_3::FT;
using Object = CGAL::Object;
using Dispatch =
CGAL::Dispatch_output_iterator,
CGAL::cpp11::tuple >,
std::back_insert_iterator > > >;
using Cell_handle = Alpha_shape_3::Cell_handle;
using Facet = Alpha_shape_3::Facet;
using Edge_3 = Alpha_shape_3::Edge;
using Vertex_handle = Alpha_shape_3::Vertex_handle;
using Vertex_list = std::vector;
// gudhi type definition
using ST = Gudhi::Simplex_tree;
using Filtration_value = ST::Filtration_value;
using Simplex_tree_vertex = ST::Vertex_handle;
using Alpha_shape_simplex_tree_map = std::map;
using Simplex_tree_vector_vertex = std::vector;
using Persistent_cohomology =
Gudhi::persistent_cohomology::Persistent_cohomology;
void usage(const std::string& progName) {
std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_weight_file path_to_the_cuboid_file "
"coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
exit(-1);
}
int main(int argc, char* const argv[]) {
// program args management
if (argc != 6) {
std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
usage(argv[0]);
}
int coeff_field_characteristic = atoi(argv[4]);
Filtration_value min_persistence = strtof(argv[5], nullptr);
// Read points from file
std::string offInputFile(argv[1]);
// Read the OFF file (input file name given as parameter) and triangulate points
Gudhi::Points_3D_off_reader off_reader(offInputFile);
// Check the read operation was correct
if (!off_reader.is_valid()) {
std::cerr << "Unable to read file " << offInputFile << std::endl;
usage(argv[0]);
}
// Retrieve the points
std::vector lp = off_reader.get_point_cloud();
// Read iso_cuboid_3 information from file
std::ifstream iso_cuboid_str(argv[3]);
double x_min, y_min, z_min, x_max, y_max, z_max;
if (iso_cuboid_str.is_open()) {
if (!(iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max)) {
std::cerr << argv[3] << " - Bad file format." << std::endl;
usage(argv[0]);
}
} else {
std::cerr << "Unable to read file " << argv[3] << std::endl;
usage(argv[0]);
}
// Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it.
if ((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min)) {
std::cerr << "The size of the cuboid in every directions is not the same." << std::endl;
exit(-1);
}
double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min);
// Read weights information from file
std::ifstream weights_ifstr(argv[2]);
std::vector wp;
if (weights_ifstr.is_open()) {
double weight = 0.0;
std::size_t index = 0;
wp.reserve(lp.size());
// Attempt read the weight in a double format, return false if it fails
while ((weights_ifstr >> weight) && (index < lp.size())) {
if ((weight >= maximal_possible_weight) || (weight < 0)) {
std::cerr << "At line " << (index + 1) << ", the weight (" << weight
<< ") is negative or more than or equal to maximal possible weight (" << maximal_possible_weight
<< ") = 1/64*cuboid length squared, which is not an acceptable input." << std::endl;
exit(-1);
}
wp.push_back(Weighted_point_3(lp[index], weight));
index++;
}
if (index != lp.size()) {
std::cerr << "Bad number of weights in file " << argv[2] << std::endl;
usage(argv[0]);
}
} else {
std::cerr << "Unable to read file " << argv[2] << std::endl;
usage(argv[0]);
}
// Define the periodic cube
P3RT3 prt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max));
// Heuristic for inserting large point sets (if pts is reasonably large)
prt.insert(wp.begin(), wp.end(), true);
// As prt won't be modified anymore switch to 1-sheeted cover if possible
if (prt.is_triangulation_in_1_sheet()) {
prt.convert_to_1_sheeted_covering();
} else {
std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl;
exit(-1);
}
std::cout << "Weighted Periodic Delaunay computed." << std::endl;
// alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
// Maybe need to set it to GENERAL mode
Alpha_shape_3 as(prt, 0, Alpha_shape_3::GENERAL);
// filtration with alpha values from alpha shape
std::vector the_objects;
std::vector the_alpha_values;
Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects),
std::back_inserter(the_alpha_values));
as.filtration_with_alpha_values(disp);
#ifdef DEBUG_TRACES
std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
#endif // DEBUG_TRACES
Alpha_shape_3::size_type count_vertices = 0;
Alpha_shape_3::size_type count_edges = 0;
Alpha_shape_3::size_type count_facets = 0;
Alpha_shape_3::size_type count_cells = 0;
// Loop on objects vector
Vertex_list vertex_list;
ST simplex_tree;
Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin();
for (auto object_iterator : the_objects) {
// Retrieve Alpha shape vertex list from object
if (const Cell_handle* cell = CGAL::object_cast(&object_iterator)) {
vertex_list = from_cell(*cell);
count_cells++;
} else if (const Facet* facet = CGAL::object_cast(&object_iterator)) {
vertex_list = from_facet(*facet);
count_facets++;
} else if (const Edge_3* edge = CGAL::object_cast(&object_iterator)) {
vertex_list = from_edge(*edge);
count_edges++;
} else if (const Vertex_handle* vertex = CGAL::object_cast(&object_iterator)) {
count_vertices++;
vertex_list = from_vertex(*vertex);
}
// Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
Simplex_tree_vector_vertex the_simplex;
for (auto the_alpha_shape_vertex : vertex_list) {
Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
if (the_map_iterator == map_cgal_simplex_tree.end()) {
// alpha shape not found
Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
#endif // DEBUG_TRACES
the_simplex.push_back(vertex);
map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
} else {
// alpha shape found
Simplex_tree_vertex vertex = the_map_iterator->second;
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
#endif // DEBUG_TRACES
the_simplex.push_back(vertex);
}
}
// Construction of the simplex_tree
Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator);
#ifdef DEBUG_TRACES
std::cout << "filtration = " << filtr << std::endl;
#endif // DEBUG_TRACES
simplex_tree.insert_simplex(the_simplex, filtr);
if (the_alpha_value_iterator != the_alpha_values.end())
++the_alpha_value_iterator;
else
std::cout << "This shall not happen" << std::endl;
}
#ifdef DEBUG_TRACES
std::cout << "vertices \t\t" << count_vertices << std::endl;
std::cout << "edges \t\t" << count_edges << std::endl;
std::cout << "facets \t\t" << count_facets << std::endl;
std::cout << "cells \t\t" << count_cells << std::endl;
std::cout << "Information of the Simplex Tree: " << std::endl;
std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " ";
std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
std::cout << " Dimension = " << simplex_tree.dimension() << " ";
#endif // DEBUG_TRACES
#ifdef DEBUG_TRACES
std::cout << "Iterator on vertices: " << std::endl;
for (auto vertex : simplex_tree.complex_vertex_range()) {
std::cout << vertex << " ";
}
#endif // DEBUG_TRACES
// Sort the simplices in the order of the filtration
simplex_tree.initialize_filtration();
std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
// Compute the persistence diagram of the complex
Persistent_cohomology pcoh(simplex_tree, true);
// initializes the coefficient field for homology
pcoh.init_coefficients(coeff_field_characteristic);
pcoh.compute_persistent_cohomology(min_persistence);
pcoh.output_diagram();
return 0;
}